[gmx-users] Box size increases in NPT

[Dr. Vitaly Chaban]

If the job is not "very parallel", it will not crash.

It is better to preequilibrate in NVT beforehand. Cyclopropylchloride
is probably a liquid at 290K, if the model is parametrized reasonably.
So it should not phase-separate.

Vitaly


On Wed, Oct 23, 2013 at 11:29 AM, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> On Oct 23, 2013 5:34 AM, "Nilesh Dhumal" <ndhumal at andrew.cmu.edu> wrote:
>>
>> Hello,
>>
>> I am running a NPT simulation for cyclopropylchloride(1) in
>> 50%water(100)+50%ethanol(100) using opls force field parameter .
>>
>> After equilibration box size increases from 20 A to 70 A.
>
> Really? Seems wildly unlikely to have occurred without crashing. Over what
> time span? How did you observe before and after? What densities do you
> measure?
>
> Mark
>
>> I used the following mdp file.
>>
>> ; RUN CONTROL PARAMETERS =
>> integrator               = sd
>> ; start time and timestep in ps =
>> tinit                    = 0
>> dt                       = 0.001
>> nsteps                   = 50000
>> ; number of steps for center of mass motion removal =
>> nstcomm                  = 100
>> ; OUTPUT CONTROL OPTIONS =
>> ; Output frequency for coords (x), velocities (v) and forces (f) =
>> nstxout                  = 0
>> nstvout                  = 0
>> nstfout                  = 0
>> ; Output frequency for energies to log file and energy file =
>> nstlog                   = 500
>> nstenergy                = 100
>> ; Output frequency and precision for xtc file =
>> nstxtcout                = 5000
>> xtc-precision            = 1000
>> ; NEIGHBORSEARCHING PARAMETERS =
>> ; nblist update frequency =
>> nstlist                  = 10
>> ; ns algorithm (simple or grid) =
>> ns_type                  = grid
>> ;OPTIONS FOR TEMPERATURE COUPLING
>> tc_grps                  = system
>> tau_t                    = 0.1
>> ref_t                    = 290;350
>> ;OPTIONS FOR PRESSURE COUPLING
>> Pcoupl                   = berendsen
>> tau_p                    = 0.5
>> compressibility          = 4.5e-05
>> ref_p                    = 1.0
>> ; OPTIONS FOR BONDS     =
>> constraints              = hbonds
>> ; Type of constraint algorithm =
>> constraint-algorithm     = Lincs
>> ; Do not constrain the start configuration =
>> unconstrained-start      = no
>> ; Relative tolerance of shake =
>> shake-tol                = 0.0001
>> ; Highest order in the expansion of the constraint coupling matrix =
>> lincs-order              = 12
>> ; Lincs will write a warning to the stderr if in one step a bond =
>> ; rotates over more degrees than =
>> lincs-warnangle          = 30
>>
>> ; Periodic boundary conditions: xyz or none =
>> pbc                      = xyz
>> ; nblist cut-off         =
>> rlist                    = 0.9
>> domain-decomposition     = no
>> ; OPTIONS FOR ELECTROSTATICS AND VDW =
>> ; Method for doing electrostatics =
>> coulombtype              = pme
>> ;rcoulomb-switch          = 0
>> rcoulomb                 = 0.9
>> ; Dielectric constant (DC) for cut-off or DC of reaction field =
>> epsilon-r                = 1
>> ; Method for doing Van der Waals =
>> vdw-type                 = switch
>> ; cut-off lengths        =
>> rvdw-switch              = 0.8
>> rvdw                     = 0.9
>> ; Apply long range dispersion corrections for Energy and Pressure =
>> DispCorr                  = EnerPres
>> ; Spacing for the PME/PPPM FFT grid =
>> fourierspacing           = 0.1
>> ; FFT grid size, when a value is 0 fourierspacing will be used =
>> fourier_nx               = 0
>> fourier_ny               = 0
>> fourier_nz               = 0
>> ; EWALD/PME/PPPM parameters =
>> pme_order                = 6
>> ewald_rtol               = 1e-06
>> epsilon_surface          = 0
>> optimize_fft             = no
>> ; Free energy control stuff
>> free_energy              = no
>>
>>
>> Nilesh
>>
>>
>>
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